Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 6 of 226
Found at i:2399101 original size:15 final size:15
Alignment explanation
Indices: 2399083--2399112 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2399073 ATATACCAAA
*
2399083 ACAAAACAAAAACCT
1 ACAAAAAAAAAACCT
2399098 ACAAAAAAAAAACCT
1 ACAAAAAAAAAACCT
2399113 GTGGCTGCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.23, G:0.00, T:0.07
Consensus pattern (15 bp):
ACAAAAAAAAAACCT
Found at i:2399709 original size:45 final size:45
Alignment explanation
Indices: 2399660--2399748 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
2399650 TCTAATTAAG
*
2399660 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATAACTCAATTTTAATTTAATAAACTATTCTCATCAAATTACT
*
2399705 TAATAACTCAATTTTAATTTAATAAACTATTCTTATCAAATTAC
1 TAATAACTCAATTTTAATTTAATAAACTATTCTCATCAAATTAC
2399749 CAAAATAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (45 bp):
TAATAACTCAATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:2399746 original size:23 final size:23
Alignment explanation
Indices: 2399675--2399746 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 23
2399665 ACTCTATTTT
*
2399675 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTTATCA
*
2399698 AATTACTTAAT-AACTCAAT-TT-T--
1 AA-T--TTAATAAACT-ATTCTTATCA
2399720 AATTTAATAAACTATTCTTATCA
1 AATTTAATAAACTATTCTTATCA
2399743 AATT
1 AATT
2399747 ACCAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 18
0.64 0.05 0.31
Matches are distributed among these distances:
19 7 0.19
20 6 0.16
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
25 5 0.14
26 7 0.19
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTTATCA
Found at i:2399777 original size:15 final size:15
Alignment explanation
Indices: 2399754--2399783 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2399744 ATTACCAAAA
2399754 TAGAGTTTATTAAAT
1 TAGAGTTTATTAAAT
*
2399769 TAGATTTTATTAAAT
1 TAGAGTTTATTAAAT
2399784 GAGAATAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAGAGTTTATTAAAT
Found at i:2400057 original size:16 final size:17
Alignment explanation
Indices: 2400036--2400067 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2400026 GGTGCCGCCA
2400036 CAGGTTTTT-TTTTTTG
1 CAGGTTTTTATTTTTTG
2400052 CAGGTTTTTATTTTTT
1 CAGGTTTTTATTTTTT
2400068 ATTTTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (17 bp):
CAGGTTTTTATTTTTTG
Found at i:2400108 original size:27 final size:29
Alignment explanation
Indices: 2400077--2400143 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
2400067 TATTTTTGGT
*
2400077 ATATTTTGGTAAAT-AAAAAAA-TTTATA
1 ATATTTTGGTAAATAAAAAAAAGGTTATA
2400104 ATATTTTGGTAAATAAAAAAAAAGGTTATA
1 ATATTTTGGTAAAT-AAAAAAAAGGTTATA
2400134 ATATTTTGGT
1 ATATTTTGGT
2400144 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 14 0.39
29 7 0.19
30 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAGGTTATA
Found at i:2402132 original size:16 final size:17
Alignment explanation
Indices: 2402100--2402137 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2402090 AATATTTTTG
**
2402100 TAATAAAATATCCTAAA
1 TAATAAAATATAATAAA
2402117 -AATAAAATATAATAAA
1 TAATAAAATATAATAAA
2402133 TAATA
1 TAATA
2402138 TTTTTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
TAATAAAATATAATAAA
Found at i:2404133 original size:9 final size:9
Alignment explanation
Indices: 2404121--2404174 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
2404111 TTCTTCTTCA
2404121 TCATCATCG
1 TCATCATCG
2404130 TCATCATCG
1 TCATCATCG
* *
2404139 TCATCCTCC
1 TCATCATCG
2404148 TCATCTTCATCG
1 TCA---TCATCG
*
2404160 TCATCATCT
1 TCATCATCG
2404169 TCATCA
1 TCATCA
2404175 ATTTCATCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
9 30 0.81
12 7 0.19
ACGTcount: A:0.20, C:0.37, G:0.06, T:0.37
Consensus pattern (9 bp):
TCATCATCG
Found at i:2404142 original size:15 final size:15
Alignment explanation
Indices: 2404118--2404197 Score: 81
Period size: 15 Copynumber: 5.3 Consensus size: 15
2404108 TTCTTCTTCT
*
2404118 TCATCATCATCGTCA
1 TCATCTTCATCGTCA
* * *
2404133 TCATCGTCATCCTCC
1 TCATCTTCATCGTCA
2404148 TCATCTTCATCGTCA
1 TCATCTTCATCGTCA
* *
2404163 TCATCTTCATCAAT-T
1 TCATCTTCATC-GTCA
*
2404178 TCATCTTCATCCTCA
1 TCATCTTCATCGTCA
2404193 TCATC
1 TCATC
2404198 CAACTCAAGC
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
14 1 0.02
15 51 0.96
16 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.04, T:0.39
Consensus pattern (15 bp):
TCATCTTCATCGTCA
Found at i:2404158 original size:30 final size:30
Alignment explanation
Indices: 2404118--2404197 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
2404108 TTCTTCTTCT
* *
2404118 TCATCATCATCGTCATCATCGTCATC-CTCC
1 TCATCTTCATCGTCATCATCGTCATCAAT-C
* *
2404148 TCATCTTCATCGTCATCATCTTCATCAATT
1 TCATCTTCATCGTCATCATCGTCATCAATC
*
2404178 TCATCTTCATCCTCATCATC
1 TCATCTTCATCGTCATCATC
2404198 CAACTCAAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 43 0.98
31 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.04, T:0.39
Consensus pattern (30 bp):
TCATCTTCATCGTCATCATCGTCATCAATC
Found at i:2404212 original size:30 final size:29
Alignment explanation
Indices: 2404118--2404213 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
2404108 TTCTTCTTCT
* * ***
2404118 TCATCATCATCGTCATCATCGTCATCCTCC
1 TCATCTTCATCCTCATCATC-TCATCAAGC
* **
2404148 TCATCTTCATCGTCATCATCTTCATCAATT
1 TCATCTTCATCCTCATCATC-TCATCAAGC
2404178 TCATCTTCATCCTCATCATC-CAACTCAAGC
1 TCATCTTCATCCTCATCATCTC-A-TCAAGC
2404208 TCATCT
1 TCATCT
2404214 CCCTGAATAG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 53 0.96
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.36
Consensus pattern (29 bp):
TCATCTTCATCCTCATCATCTCATCAAGC
Found at i:2411748 original size:30 final size:30
Alignment explanation
Indices: 2411712--2411768 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2411702 TACTCTTAGA
2411712 TGATGCTGTAGTATCAGAAAAAAAGGTAGG
1 TGATGCTGTAGTATCAGAAAAAAAGGTAGG
* *
2411742 TGATGCTGTGGTATCAGGAAAAAAGGT
1 TGATGCTGTAGTATCAGAAAAAAAGGT
2411769 GGAGGAGACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.25
Consensus pattern (30 bp):
TGATGCTGTAGTATCAGAAAAAAAGGTAGG
Found at i:2431899 original size:6 final size:6
Alignment explanation
Indices: 2431888--2431914 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2431878 CAAAACTGAG
2431888 AATTCC AATTCC AATTCC AATTCC AAT
1 AATTCC AATTCC AATTCC AATTCC AAT
2431915 ATATATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (6 bp):
AATTCC
Found at i:2433066 original size:20 final size:21
Alignment explanation
Indices: 2433041--2433094 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
2433031 TTTACTCAAA
2433041 CTAATTTTTTATTAAAA-TTT
1 CTAATTTTTTATTAAAATTTT
** *
2433061 CTAATTGATTCTTAAAATTTT
1 CTAATTTTTTATTAAAATTTT
2433082 CT-ATTTTTATATT
1 CTAATTTTT-TATT
2433095 TTCAAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
CTAATTTTTTATTAAAATTTT
Found at i:2433675 original size:30 final size:29
Alignment explanation
Indices: 2433635--2433699 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
2433625 GTTAATAAAT
2433635 TATA-AAAATTAGATA-AAATTAAAATTTTA
1 TATATAAAATTAGA-ACAAATTAAAA-TTTA
*
2433664 TATATAAAATTATAACAAATTAAAATTTA
1 TATATAAAATTAGAACAAATTAAAATTTA
*
2433693 TGTATAA
1 TATATAA
2433700 TTTTAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (29 bp):
TATATAAAATTAGAACAAATTAAAATTTA
Found at i:2437163 original size:14 final size:15
Alignment explanation
Indices: 2437144--2437173 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2437134 TTTTTCACTT
2437144 TAATAA-TATAAAAA
1 TAATAATTATAAAAA
2437158 TAATAATTATAAAAA
1 TAATAATTATAAAAA
2437173 T
1 T
2437174 GGGCTCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATAATTATAAAAA
Found at i:2437341 original size:13 final size:13
Alignment explanation
Indices: 2437323--2437376 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
2437313 AGTTCTTTAT
2437323 TACTTTTGAAAAG
1 TACTTTTGAAAAG
*
2437336 TACTTTTGAAAAA
1 TACTTTTGAAAAG
* *
2437349 TGC-TGTGAAAAAAG
1 TACTTTTG--AAAAG
2437363 TACTTTTGAAAAG
1 TACTTTTGAAAAG
2437376 T
1 T
2437377 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 3 0.09
13 20 0.62
14 6 0.19
15 3 0.09
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:2441228 original size:21 final size:21
Alignment explanation
Indices: 2441204--2441262 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2441194 AGTGCTAAAT
2441204 AGAAACCCATAAGGGTTGAAC
1 AGAAACCCATAAGGGTTGAAC
* * * * *
2441225 AGAAGCTCGTAAGAGCTGAAC
1 AGAAACCCATAAGGGTTGAAC
*
2441246 AGAAACCTATAAGGGTT
1 AGAAACCCATAAGGGTT
2441263 AAACTGAAGC
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AGAAACCCATAAGGGTTGAAC
Found at i:2441228 original size:42 final size:42
Alignment explanation
Indices: 2441181--2441286 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
2441171 CGAAGGCTGC
* * *
2441181 ACAGAAGCACATAAGTGCTAAATAGAAACCCATAAGGGTTGA
1 ACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGGGTTAA
* * * *
2441223 ACAGAAGCTCGTAAGAGCTGAACAGAAACCTATAAGGGTTAA
1 ACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGGGTTAA
* *
2441265 ACTGAAGCACAAAAGAGCTAAA
1 ACAGAAGCACATAAGAGCTAAA
2441287 GTAAAACTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (42 bp):
ACAGAAGCACATAAGAGCTAAACAGAAACCCATAAGGGTTAA
Found at i:2444612 original size:12 final size:12
Alignment explanation
Indices: 2444595--2444621 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2444585 TAGGTATATA
2444595 ATTATTATAATT
1 ATTATTATAATT
2444607 ATTATTATAATT
1 ATTATTATAATT
2444619 ATT
1 ATT
2444622 TATTCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTATAATT
Found at i:2446065 original size:51 final size:51
Alignment explanation
Indices: 2446001--2446111 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 51
2445991 TGTGCCGACT
** *
2446001 ACTGTTATTGTTACCGATTCGGCACTTCATGTGTCGAATACTGTTACTGTC
1 ACTGTTACCGTTACCGATTCGACACTTCATGTGTCGAATACTGTTACTGTC
** *
2446052 ACTGTTACCGTTACCGATTCGACACTTTGTGTGTCGAATACTGTTACTGTT
1 ACTGTTACCGTTACCGATTCGACACTTCATGTGTCGAATACTGTTACTGTC
2446103 ACTGATTAC
1 ACTG-TTAC
2446112 TATTTACTGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 49 0.92
52 4 0.08
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.39
Consensus pattern (51 bp):
ACTGTTACCGTTACCGATTCGACACTTCATGTGTCGAATACTGTTACTGTC
Found at i:2446275 original size:2 final size:2
Alignment explanation
Indices: 2446268--2446298 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2446258 AATAAGAATG
2446268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2446299 ATTAATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2446320 original size:15 final size:16
Alignment explanation
Indices: 2446275--2446324 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
2446265 ATGATATATA
*
2446275 TATATATATATATATA-
1 TATATATA-ATAAATAG
*
2446291 TATATATAATTAATAG
1 TATATATAATAAATAG
2446307 TATA-ATAATAAATAG
1 TATATATAATAAATAG
2446322 TAT
1 TAT
2446325 TAGTTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
TATATATAATAAATAG
Found at i:2470070 original size:26 final size:26
Alignment explanation
Indices: 2470009--2470070 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2469999 TGAAATATAA
* *
2470009 TTAAATTATATATTATTTTATTAAAT
1 TTAAATAATATATAATTTTATTAAAT
**
2470035 TATATTTAATA-ATAATTTTATTAAAAT
1 T-TAAATAATATATAATTTTATT-AAAT
2470062 TTAAATAAT
1 TTAAATAAT
2470071 TATTTACCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAATAATATATAATTTTATTAAAT
Found at i:2470075 original size:23 final size:25
Alignment explanation
Indices: 2470020--2470075 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
2470010 TAAATTATAT
*
2470020 ATTATTTTATTAAATTATATTTAATA
1 ATTATTTTATTAAA-TATATTAAATA
*
2470046 ATAATTTTATTAAA-AT-TTAAATA
1 ATTATTTTATTAAATATATTAAATA
2470069 ATTATTT
1 ATTATTT
2470076 ACCTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.44
24 2 0.07
26 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTATTTTATTAAATATATTAAATA
Found at i:2473485 original size:22 final size:23
Alignment explanation
Indices: 2473415--2473487 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
2473405 TTTCCATGCA
2473415 TGCAAGTGATAGTGGCACTACGG
1 TGCAAGTGATAGTGGCACTACGG
* *
2473438 TGCAAGTGATAGCGGCACTACAG
1 TGCAAGTGATAGTGGCACTACGG
* *
2473461 TGCAAGTG-TTGTGGCACTTCGG
1 TGCAAGTGATAGTGGCACTACGG
2473483 TGCAA
1 TGCAA
2473488 AATGACATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 15 0.34
23 29 0.66
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (23 bp):
TGCAAGTGATAGTGGCACTACGG
Found at i:2474972 original size:20 final size:20
Alignment explanation
Indices: 2474947--2474988 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2474937 GAAATAATAA
*
2474947 ATCTATATAGATCAGTAAGT
1 ATCTATATAGATCAATAAGT
2474967 ATCTATATAGATCAATAAGT
1 ATCTATATAGATCAATAAGT
2474987 AT
1 AT
2474989 AGGGACTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCTATATAGATCAATAAGT
Found at i:2476182 original size:16 final size:16
Alignment explanation
Indices: 2476155--2476195 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
2476145 ATAGTAAAAA
2476155 TATAATTTTATTATTTT
1 TATAA-TTTATTATTTT
*
2476172 TATAATTTATTGTTTT
1 TATAATTTATTATTTT
2476188 TATAATTT
1 TATAATTT
2476196 TTAAGTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATAATTTATTATTTT
Found at i:2477268 original size:30 final size:30
Alignment explanation
Indices: 2477208--2477270 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2477198 ACTTATTTTA
*
2477208 TTGTTAATTTTGTTATTATTTTTAAGACAT
1 TTGTTAATTTTGTTATTATTTTTAAAACAT
*
2477238 TTGTTAATTTTTTTATTA-TTTTAGAAACAT
1 TTGTTAATTTTGTTATTATTTTTA-AAACAT
2477268 TTG
1 TTG
2477271 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTTAAAACAT
Found at i:2480536 original size:5 final size:5
Alignment explanation
Indices: 2480526--2480571 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
2480516 CTTAGATGTT
* * *
2480526 TTATA TTATA TTATA TTATA TTGTA TTGTA TTGTA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA T
2480572 AAATTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:2480739 original size:20 final size:20
Alignment explanation
Indices: 2480714--2480752 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2480704 ATATTATTAT
2480714 AACAAAAAAAATAAAAGAAA
1 AACAAAAAAAATAAAAGAAA
**
2480734 AACAAATGAAATAAAAGAA
1 AACAAAAAAAATAAAAGAA
2480753 TAGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (20 bp):
AACAAAAAAAATAAAAGAAA
Found at i:2481759 original size:21 final size:21
Alignment explanation
Indices: 2481704--2481791 Score: 99
Period size: 21 Copynumber: 4.2 Consensus size: 21
2481694 TTATCGACTT
2481704 TGTCG-ATCAGGCACTTTATG
1 TGTCGTATCAGGCACTTTATG
2481724 TGTCGTATCTCAGGCACTTTATG
1 TGTCGTA--TCAGGCACTTTATG
* **
2481747 TGTCGTATCAGGCACCTCGTG
1 TGTCGTATCAGGCACTTTATG
* *
2481768 TGTCGTTTCAGGTAC-TTATG
1 TGTCGTATCAGGCACTTTATG
2481788 TGTC
1 TGTC
2481792 TATATTGATC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.21
21 25 0.43
23 21 0.36
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (21 bp):
TGTCGTATCAGGCACTTTATG
Found at i:2481760 original size:44 final size:40
Alignment explanation
Indices: 2481704--2481791 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 40
2481694 TTATCGACTT
* *
2481704 TGTCGATCAGGCACTTTATGTGTCGTATCTCAGGCACTTTATG
1 TGTCGATCAGGCACCTCATGTGTCGT-T-TCAGGCAC-TTATG
* *
2481747 TGTCGTATCAGGCACCTCGTGTGTCGTTTCAGGTACTTATG
1 TGTCG-ATCAGGCACCTCATGTGTCGTTTCAGGCACTTATG
2481788 TGTC
1 TGTC
2481792 TATATTGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
41 9 0.22
42 7 0.17
43 6 0.15
44 18 0.45
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (40 bp):
TGTCGATCAGGCACCTCATGTGTCGTTTCAGGCACTTATG
Found at i:2492636 original size:22 final size:22
Alignment explanation
Indices: 2492608--2492679 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
2492598 AATAAAAACC
2492608 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
2492630 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
2492652 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
2492674 CTCATG
1 CTCATG
2492680 TTTGAACAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:2497522 original size:2 final size:2
Alignment explanation
Indices: 2497515--2497549 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2497505 TGCTGGAAAA
2497515 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2497550 TGTGTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2504675 original size:36 final size:36
Alignment explanation
Indices: 2504584--2504676 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
2504574 TTTTGGTCCC
* * * *
2504584 ACACATGGGGAAAGGCTTACGTGAGGTCCTGCTCCT
1 ACACATGGGGGAAGGCTTATGGGAGGTCCTACTCCT
* * *
2504620 ATACATGGGAGAAGGCTTATGGGAGGTCGTACTCCT
1 ACACATGGGGGAAGGCTTATGGGAGGTCCTACTCCT
2504656 ACACATGGGGGAAGGCTTATG
1 ACACATGGGGGAAGGCTTATG
2504677 AGAAGTGATA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (36 bp):
ACACATGGGGGAAGGCTTATGGGAGGTCCTACTCCT
Found at i:2506698 original size:23 final size:23
Alignment explanation
Indices: 2506671--2506792 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
2506661 AGTGTTATTG
2506671 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
2506694 TTCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2506717 ATCAGTGGTAGCTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
2506740 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
2506763 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2506786 ATCAGTG
1 ATCAGTG
2506793 TGGCACTTAT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2506723 original size:46 final size:46
Alignment explanation
Indices: 2506671--2506792 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
2506661 AGTGTTATTG
2506671 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
* * *
2506717 ATCAGTGGTAGCTTCGGTTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
*
2506763 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
2506793 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACAGCTACAT
Found at i:2541259 original size:2 final size:2
Alignment explanation
Indices: 2541254--2541285 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2541244 ACACACACAC
2541254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2541286 TAAGTTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2544024 original size:18 final size:19
Alignment explanation
Indices: 2543990--2544032 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2543980 ATTACAAAAA
*
2543990 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
2544009 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
2544027 AAAAAT
1 AAAAAT
2544033 TTTAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:2554729 original size:17 final size:17
Alignment explanation
Indices: 2554700--2554732 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2554690 TGAATAAAAT
2554700 AATAATAATTTTTTTTG
1 AATAATAATTTTTTTTG
2554717 AATAA-AATATTTTTTT
1 AATAATAAT-TTTTTTT
2554733 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATAATAATTTTTTTTG
Found at i:2554835 original size:19 final size:19
Alignment explanation
Indices: 2554811--2554936 Score: 71
Period size: 19 Copynumber: 6.3 Consensus size: 19
2554801 GGCGCCAATG
2554811 AATATTGTAATTTTGTATT
1 AATATTGTAATTTTGTATT
*
2554830 AATATTGTAATTAT-T-TT
1 AATATTGTAATTTTGTATT
* *
2554847 -ATAAT-TAAATTTGTATTT
1 AATATTGTAATTTTGTA-TT
* *
2554865 ATAGTTTTGGATTAGTATTTTGTATG
1 A-A-TATT-G--TA--ATTTTGTATT
*
2554891 AATATTGTAATTTTTTATAT
1 AATATTGTAATTTTGTAT-T
*
2554911 GAATATTGTAATTTTGTATG
1 -AATATTGTAATTTTGTATT
2554931 AATATT
1 AATATT
2554937 CATTGGCGCC
Statistics
Matches: 80, Mismatches: 13, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
15 5 0.06
16 5 0.06
17 2 0.03
18 3 0.04
19 27 0.34
20 1 0.01
21 21 0.26
23 1 0.01
24 3 0.04
25 3 0.04
26 2 0.03
27 7 0.09
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (19 bp):
AATATTGTAATTTTGTATT
Found at i:2554911 original size:21 final size:21
Alignment explanation
Indices: 2554882--2554925 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2554872 TGGATTAGTA
*
2554882 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
2554903 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
2554924 TT
1 TT
2554926 GTATGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:2554966 original size:27 final size:27
Alignment explanation
Indices: 2554935--2555001 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
2554925 TGTATGAATA
2554935 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
* *
2554962 TTCATTGGCGCCTCTCTGTGAGGCATC
1 TTCATTGGCGCCTCTCTATGAGGCACC
2554989 TTCATTGGCGCCT
1 TTCATTGGCGCCT
2555002 ACCTGATAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.12, C:0.31, G:0.24, T:0.33
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:2560588 original size:11 final size:9
Alignment explanation
Indices: 2560555--2560579 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2560545 AAATTTTATT
2560555 TTTTATATG
1 TTTTATATG
2560564 TTTTATATG
1 TTTTATATG
2560573 TTTTATA
1 TTTTATA
2560580 CTTGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTTTATATG
Found at i:2563643 original size:6 final size:6
Alignment explanation
Indices: 2563634--2563664 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2563624 TTTATTTTAT
*
2563634 TTAATA TTAATA TTAATA GTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA TTAATA T
2563665 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TTAATA
Found at i:2564459 original size:10 final size:10
Alignment explanation
Indices: 2564444--2564560 Score: 60
Period size: 10 Copynumber: 11.6 Consensus size: 10
2564434 TGACATGTGG
2564444 TAAAAAATTA
1 TAAAAAATTA
2564454 TAAAAAA-TA
1 TAAAAAATTA
* **
2564463 TTTAAATTTTA
1 -TAAAAAATTA
*
2564474 TTAAAAATTA
1 TAAAAAATTA
*
2564484 GAAAAAATTA
1 TAAAAAATTA
**
2564494 T-AAAAATCG
1 TAAAAAATTA
*
2564503 TAAAAGAAATA
1 TAAAA-AATTA
*
2564514 TAAAAAAATA
1 TAAAAAATTA
* **
2564524 GTGAAATTTTA
1 -TAAAAAATTA
*
2564535 T-AAAAATCA
1 TAAAAAATTA
2564544 TAAAAAATATA
1 TAAAAAAT-TA
2564555 TAAAAA
1 TAAAAA
2564561 TGCATCAAAA
Statistics
Matches: 79, Mismatches: 21, Indels: 13
0.70 0.19 0.12
Matches are distributed among these distances:
9 15 0.19
10 42 0.53
11 22 0.28
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:2564481 original size:30 final size:29
Alignment explanation
Indices: 2564446--2564558 Score: 104
Period size: 30 Copynumber: 3.8 Consensus size: 29
2564436 ACATGTGGTA
*
2564446 AAAAATTATAAAAAATATTTAAATTTTATT
1 AAAAATTATAAAAAATATATAAATTTTA-T
* * **
2564476 AAAAATTAGAAAAAATTATAAAAATCGTA-
1 AAAAATTATAAAAAA-TATATAAATTTTAT
*
2564505 AAAGAAATATAAAAAA-ATAGTGAAATTTTAT
1 AAA-AATTATAAAAAATATA-T-AAATTTTAT
*
2564536 AAAAATCATAAAAAATATATAAA
1 AAAAATTATAAAAAATATATAAA
2564559 AATGCATCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
28 3 0.05
29 6 0.09
30 41 0.63
31 15 0.23
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAAATTATAAAAAATATATAAATTTTAT
Found at i:2564521 original size:41 final size:41
Alignment explanation
Indices: 2564443--2564560 Score: 107
Period size: 41 Copynumber: 2.9 Consensus size: 41
2564433 GTGACATGTG
** * * * *
2564443 GTAAAAAATTATAAAAAAT-ATTTAAATTTTATTAAAAATTA
1 GTAAAAAATTAT-AAAAATCATAAAAAATATATAAAAAAATA
*
2564484 G-AAAAAATTATAAAAATCGTAAAAGAA-ATATAAAAAAATA
1 GTAAAAAATTATAAAAATCATAAAA-AATATATAAAAAAATA
* **
2564524 GTGAAATTTTATAAAAATCATAAAAAATATATAAAAA
1 GTAAAAAATTATAAAAATCATAAAAAATATATAAAAA
2564561 TGCATCAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
39 6 0.10
40 26 0.42
41 30 0.48
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (41 bp):
GTAAAAAATTATAAAAATCATAAAAAATATATAAAAAAATA
Found at i:2564550 original size:61 final size:59
Alignment explanation
Indices: 2564443--2564561 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 59
2564433 GTGACATGTG
* * *
2564443 GTAAAAAATTATAAAAAATATTTAAATTTTATTAAAAATTAGAAAAAAT-TATAAAAATC
1 GTAAAAAAATATAAAAAATAGTGAAATTTTATTAAAAATT-GAAAAAATATATAAAAATC
2564502 GTAAAAGAAATATAAAAAAATAGTGAAATTTTA-TAAAAATCAT-AAAAAATATATAAAAAT
1 GTAAAA-AAATAT-AAAAAATAGTGAAATTTTATTAAAAAT--TGAAAAAATATATAAAAAT
2564562 GCATCAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
59 6 0.12
60 19 0.37
61 26 0.50
62 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (59 bp):
GTAAAAAAATATAAAAAATAGTGAAATTTTATTAAAAATTGAAAAAATATATAAAAATC
Found at i:2564822 original size:36 final size:36
Alignment explanation
Indices: 2564776--2564849 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
2564766 CTTTACATTA
2564776 TTATAATTCTCTTACGACTTTATAAAATATTACAAT
1 TTATAATTCTCTTACGACTTTATAAAATATTACAAT
2564812 TTATAATTCTCTTACGACTTTATAAAATATTACAAT
1 TTATAATTCTCTTACGACTTTATAAAATATTACAAT
2564848 TT
1 TT
2564850 TACATTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.46
Consensus pattern (36 bp):
TTATAATTCTCTTACGACTTTATAAAATATTACAAT
Found at i:2564826 original size:18 final size:19
Alignment explanation
Indices: 2564776--2564836 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
2564766 CTTTACATTA
2564776 TTATAATTCTCTTACGACT
1 TTATAATTCTCTTACGACT
** * *
2564795 TTATAA-AATATTAC-AAT
1 TTATAATTCTCTTACGACT
2564812 TTATAATTCTCTTACGACT
1 TTATAATTCTCTTACGACT
2564831 TTATAA
1 TTATAA
2564837 AATATTACAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 8 0.25
18 10 0.31
19 14 0.44
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (19 bp):
TTATAATTCTCTTACGACT
Found at i:2564844 original size:18 final size:18
Alignment explanation
Indices: 2564787--2564844 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2564777 TATAATTCTC
2564787 TTACGACTTTATAAAATA
1 TTACGACTTTATAAAATA
* ** *
2564805 TTAC-AATTTATAATTCTC
1 TTACGACTTTATAA-AATA
2564823 TTACGACTTTATAAAATA
1 TTACGACTTTATAAAATA
2564841 TTAC
1 TTAC
2564845 AATTTTACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 8 0.27
18 14 0.47
19 8 0.27
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (18 bp):
TTACGACTTTATAAAATA
Found at i:2564851 original size:18 final size:17
Alignment explanation
Indices: 2564794--2564849 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2564784 CTCTTACGAC
2564794 TTTATAAAATATTACAA
1 TTTATAAAATATTACAA
** * *
2564811 TTTATAATTCTCTTACGAC
1 TTTATAA-AATATTAC-AA
2564830 TTTATAAAATATTACAA
1 TTTATAAAATATTACAA
2564847 TTT
1 TTT
2564850 TACATTTTAC
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
17 11 0.38
18 10 0.34
19 8 0.28
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTATAAAATATTACAA
Found at i:2564954 original size:19 final size:18
Alignment explanation
Indices: 2564907--2564959 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
2564897 TTATTTCTAT
*
2564907 TTTTTAAAATAATTTAATA
1 TTTTTATAA-AATTTAATA
2564926 -TTTTATTAAAATTTAATAA
1 TTTTTA-TAAAATTTAAT-A
*
2564945 TTTTTATAAATTTTA
1 TTTTTATAAAATTTA
2564960 TTAGTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 13 0.45
19 11 0.38
20 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTATAAAATTTAATA
Found at i:2564955 original size:18 final size:18
Alignment explanation
Indices: 2564917--2564957 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2564907 TTTTTAAAAT
*
2564917 AATTTAATATTTTATTAA
1 AATTTAATAATTTATTAA
2564935 AATTTAATAATTT-TTATA
1 AATTTAATAATTTATTA-A
2564953 AATTT
1 AATTT
2564958 TATTAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAATAATTTATTAA
Found at i:2567660 original size:26 final size:26
Alignment explanation
Indices: 2567600--2567660 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
2567590 AAAGAAAATT
*
2567600 TAAAATATTATTTTATTTTACTTTGAA
1 TAAAATATTATTTTATTTTAC-TTCAA
*
2567627 -AAAGTATTATTTTATTTTTA-TTCAA
1 TAAAATATTATTTTA-TTTTACTTCAA
*
2567652 TAAATTATT
1 TAAAATATT
2567661 CTTATCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 4 0.14
26 20 0.69
27 5 0.17
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
TAAAATATTATTTTATTTTACTTCAA
Found at i:2576756 original size:15 final size:15
Alignment explanation
Indices: 2576717--2576774 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
2576707 TAAATTCAGT
* *
2576717 ACTTAAATTTTCAAT
1 ACTTAATTTTTCAAC
*
2576732 ATTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
* *
2576747 ACTTATTTTTTCAGC
1 ACTTAATTTTTCAAC
2576762 ACTTAATTTTTCA
1 ACTTAATTTTTCA
2576775 GTTTATCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.52
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:2576775 original size:15 final size:15
Alignment explanation
Indices: 2576711--2576775 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
2576701 ATAACTTAAA
* *
2576711 TTCAGTACTTAAATT
1 TTCAGCACTTAATTT
** *
2576726 TTCAATATTTAATTT
1 TTCAGCACTTAATTT
* *
2576741 TTCAACACTTATTTT
1 TTCAGCACTTAATTT
2576756 TTCAGCACTTAATTT
1 TTCAGCACTTAATTT
2576771 TTCAG
1 TTCAG
2576776 TTTATCAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (15 bp):
TTCAGCACTTAATTT
Found at i:2592829 original size:5 final size:5
Alignment explanation
Indices: 2592819--2592843 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2592809 GAAAAACAAC
2592819 TATGA TATGA TATGA TATGA TATGA
1 TATGA TATGA TATGA TATGA TATGA
2592844 ATTACTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TATGA
Found at i:2599028 original size:21 final size:22
Alignment explanation
Indices: 2598989--2599030 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2598979 CATTTAATGA
*
2598989 ATTTTTTAAAATTTTAAAAAAT
1 ATTTTTTAAAATTTAAAAAAAT
2599011 ATTTTTTAAAA-TTAAAAAAA
1 ATTTTTTAAAATTTAAAAAAA
2599031 GGTATAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTTTAAAATTTAAAAAAAT
Found at i:2600446 original size:22 final size:22
Alignment explanation
Indices: 2600421--2600462 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2600411 GATTTGATGG
2600421 ATATAATATC-AATAATTTAAGA
1 ATATAAT-TCAAATAATTTAAGA
*
2600443 ATATAATTCAAATATTTTAA
1 ATATAATTCAAATAATTTAA
2600463 AGTTTAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATAATTCAAATAATTTAAGA
Found at i:2607198 original size:15 final size:16
Alignment explanation
Indices: 2607170--2607202 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2607160 TTAGTATTTT
2607170 TAAATTATATTTAAAA
1 TAAATTATATTTAAAA
2607186 TAAATTA-ATTTAAAA
1 TAAATTATATTTAAAA
2607201 TA
1 TA
2607203 CATGAGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTATATTTAAAA
Found at i:2607537 original size:18 final size:18
Alignment explanation
Indices: 2607510--2607551 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2607500 TTGGTGGGTT
*
2607510 AAAT-TAAAAAAATACTTA
1 AAATATAAAATAATA-TTA
*
2607528 AAATATAAAATATTATTA
1 AAATATAAAATAATATTA
2607546 AAATAT
1 AAATAT
2607552 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAAAATAATATTA
Found at i:2607547 original size:11 final size:11
Alignment explanation
Indices: 2607533--2607570 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2607523 ACTTAAAATA
2607533 TAAAATATTAT
1 TAAAATATTAT
2607544 TAAAATATTATT
1 TAAAATATTA-T
*
2607556 TTAAAT-TTAT
1 TAAAATATTAT
2607566 TAAAA
1 TAAAA
2607571 ACTTGTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.21
11 13 0.54
12 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAAATATTAT
Found at i:2611010 original size:45 final size:46
Alignment explanation
Indices: 2610956--2611065 Score: 195
Period size: 46 Copynumber: 2.4 Consensus size: 46
2610946 TCACTTGTCA
*
2610956 TTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCAC
1 TTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCAC
*
2611001 TTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCAC
1 TTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCAC
2611047 TTGATCAGATAAGTGTAGC
1 TTGATCAGATAAGTGTAGC
2611066 CACTTATCAC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 20 0.32
46 42 0.68
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (46 bp):
TTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCAC
Found at i:2611048 original size:46 final size:45
Alignment explanation
Indices: 2610942--2611175 Score: 243
Period size: 37 Copynumber: 5.6 Consensus size: 45
2610932 CATATGACCT
*
2610942 CTTATCAC-TTGTCA-TTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2610985 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
2611031 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
2611068 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** *
2611105 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
2611151 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
2611176 AGTACTCAAA
Statistics
Matches: 169, Mismatches: 9, Indels: 23
0.84 0.04 0.11
Matches are distributed among these distances:
37 64 0.38
39 2 0.01
40 3 0.02
41 1 0.01
42 1 0.01
43 10 0.06
44 6 0.04
45 20 0.12
46 62 0.37
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2614161 original size:21 final size:21
Alignment explanation
Indices: 2614121--2614169 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2614111 ATAGTAAGAA
*
2614121 TAAAAATGTTTCCTAAAATTT
1 TAAAAATGTTTCCTAAAATTG
** *
2614142 TAAAAATGTTTGGTATAATTG
1 TAAAAATGTTTCCTAAAATTG
2614163 TAAAAAT
1 TAAAAAT
2614170 AATAATTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAAAATGTTTCCTAAAATTG
Found at i:2624426 original size:8 final size:7
Alignment explanation
Indices: 2624401--2624445 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
2624391 GCAAAAAGAG
*
2624401 AACAGAA
1 AACAAAA
2624408 AACAAAA
1 AACAAAA
2624415 AACAATAA
1 AACAA-AA
2624423 AACAAAA
1 AACAAAA
2624430 AACAATAA
1 AACAA-AA
2624438 AACAAAA
1 AACAAAA
2624445 A
1 A
2624446 GCCAAAGGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
7 21 0.60
8 14 0.40
ACGTcount: A:0.80, C:0.13, G:0.02, T:0.04
Consensus pattern (7 bp):
AACAAAA
Found at i:2624426 original size:15 final size:15
Alignment explanation
Indices: 2624406--2624445 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2624396 AAGAGAACAG
2624406 AAAACAAAAAACAAT
1 AAAACAAAAAACAAT
2624421 AAAACAAAAAACAAT
1 AAAACAAAAAACAAT
2624436 AAAACAAAAA
1 AAAACAAAAA
2624446 GCCAAAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.05
Consensus pattern (15 bp):
AAAACAAAAAACAAT
Found at i:2626792 original size:2 final size:2
Alignment explanation
Indices: 2626785--2626811 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2626775 TTCTCAATGC
2626785 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2626812 CATGTTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2638696 original size:26 final size:25
Alignment explanation
Indices: 2638659--2638708 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2638649 TGAAGGTAAA
2638659 CATTAATTTT-AATTATTAATTAAAAG
1 CATTAATTTTAAATT-TT-ATTAAAAG
2638685 CATT-ATTATTAAATTTTATTAAAA
1 CATTAATT-TTAAATTTTATTAAAA
2638709 TTTGAGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 10 0.45
26 8 0.36
27 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
CATTAATTTTAAATTTTATTAAAAG
Found at i:2642631 original size:2 final size:2
Alignment explanation
Indices: 2642624--2642653 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2642614 TATAAAGCAA
2642624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2642654 TGAAAGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2647127 original size:42 final size:42
Alignment explanation
Indices: 2647057--2647142 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
2647047 TGCCTGAACC
2647057 ATGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAA
1 ATGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAA
* * *
2647099 ATGAAGGGTGGGTGGAAA-CTTAGCAGCTCCCAAAATGGCCAA
1 ATGAAGGGTGGGT-AAAAGCTAAGAAGCTCCCAAAATGGCCAA
2647141 AT
1 AT
2647143 AAACCAGAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.16
Consensus pattern (42 bp):
ATGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAA
Found at i:2647997 original size:2 final size:2
Alignment explanation
Indices: 2647992--2648021 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2647982 CTTTGTGTGA
2647992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2648022 TCCTTGCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2664306 original size:21 final size:21
Alignment explanation
Indices: 2664274--2664342 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
2664264 GCCCGGCCCG
2664274 TTTTTAATTAAAATTAAAATTA
1 TTTTTAA-TAAAATTAAAATTA
*
2664296 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAA-TTA
* *
2664318 TTGTTAGTAAAATTATAAAATTA
1 TTTTTAATAAAA-T-TAAAATTA
2664341 TT
1 TT
2664343 AATTGTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 11 0.28
22 19 0.47
23 5 0.12
24 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTTTAATAAAATTAAAATTA
Found at i:2664405 original size:66 final size:59
Alignment explanation
Indices: 2664329--2664454 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
2664319 TGTTAGTAAA
* * *
2664329 ATTA-TAAAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 ATTAGTAAAATTATAAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
* *
2664386 ATTAGTAAATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
1 ATTAGTAAAATTATAAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
*
2664445 ATTAATAAAA
1 ATTAGTAAAA
2664455 CAAACTTGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 4 0.07
58 8 0.13
59 49 0.80
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (59 bp):
ATTAGTAAAATTATAAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTG
Found at i:2664449 original size:30 final size:30
Alignment explanation
Indices: 2664356--2664450 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
2664346 TGTTAATTGT
*
2664356 ATTAATTGTTGTAATAAAATCTAACATTTG
1 ATTAATTGTTGTAACAAAATCTAACATTTG
* ** * ** *
2664386 ATTAGTAAATT-TATC-AAAT-TATTAATTG
1 ATTAAT-TGTTGTAACAAAATCTAACATTTG
2664414 TATTAATTGTTGTAACAAAATCTAACATTTG
1 -ATTAATTGTTGTAACAAAATCTAACATTTG
2664445 ATTAAT
1 ATTAAT
2664451 AAAACAAACT
Statistics
Matches: 45, Mismatches: 15, Indels: 10
0.64 0.21 0.14
Matches are distributed among these distances:
28 8 0.18
29 12 0.27
30 17 0.38
31 8 0.18
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.44
Consensus pattern (30 bp):
ATTAATTGTTGTAACAAAATCTAACATTTG
Found at i:2664557 original size:22 final size:24
Alignment explanation
Indices: 2664517--2664560 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2664507 AAATAAACTT
2664517 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
2664541 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
2664561 AATATTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:2668496 original size:3 final size:3
Alignment explanation
Indices: 2668490--2668516 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2668480 AAAAAAAGTA
2668490 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2668517 CAATTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2672725 original size:19 final size:18
Alignment explanation
Indices: 2672686--2672734 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
2672676 TTTATAATTA
2672686 TAATTTATAAATATATTT
1 TAATTTATAAATATATTT
*
2672704 TAATGTTATATATAT-TTAT
1 TAAT-TTATAAATATATT-T
*
2672723 TAATATATAAAT
1 TAATTTATAAAT
2672735 TATAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTTATAAATATATTT
Found at i:2674867 original size:25 final size:25
Alignment explanation
Indices: 2674827--2674917 Score: 139
Period size: 25 Copynumber: 3.6 Consensus size: 25
2674817 TTATCATGCA
2674827 CTAATGAA-CAGAGAGCACTGACGTG
1 CTAAT-AATCAGAGAGCACTGACGTG
* *
2674852 CTAGTAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
2674877 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
2674902 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
2674918 GCGCTAAGGT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 2 0.03
25 58 0.97
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGACGTG
Found at i:2675823 original size:26 final size:26
Alignment explanation
Indices: 2675794--2675877 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 26
2675784 AAATCTCAAA
2675794 TTTTCTTTCTTTCCTTCCCTTTTTCT
1 TTTTCTTTCTTTCCTTCCCTTTTTCT
*
2675820 TTTTCTTTCCTTT-CTCCCCTGTTTTCGT
1 TTTTCTTT-CTTTCCTTCCCT-TTTTC-T
* *
2675848 TTTGCTATTCTGTTTCTATTCCCTTTTTCT
1 TTTTCT-TTC--TTTC-CTTCCCTTTTTCT
2675878 ATCTTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
26 14 0.30
27 9 0.20
28 7 0.15
29 2 0.04
30 4 0.09
31 5 0.11
32 5 0.11
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (26 bp):
TTTTCTTTCTTTCCTTCCCTTTTTCT
Found at i:2676418 original size:25 final size:25
Alignment explanation
Indices: 2676390--2676437 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2676380 CAAACGAACC
2676390 ATATCAGGA-AGCTCACAAAGAGCCT
1 ATATCAGGACA-CTCACAAAGAGCCT
* *
2676415 ATATCGGGACACTCATAAAGAGC
1 ATATCAGGACACTCACAAAGAGC
2676438 TGCGGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (25 bp):
ATATCAGGACACTCACAAAGAGCCT
Found at i:2676935 original size:21 final size:21
Alignment explanation
Indices: 2676911--2676954 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2676901 AGTAAATTTA
* *
2676911 ATTCATTTTAATACAATTCAC
1 ATTCAATTCAATACAATTCAC
* *
2676932 ATTCAATTCCATCCAATTCAC
1 ATTCAATTCAATACAATTCAC
2676953 AT
1 AT
2676955 CCTAGGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTCAATTCAATACAATTCAC
Found at i:2676940 original size:11 final size:11
Alignment explanation
Indices: 2676924--2676956 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2676914 CATTTTAATA
*
2676924 CAATTCACATT
1 CAATTCACATC
2676935 CAATTC-CATC
1 CAATTCACATC
2676945 CAATTCACATC
1 CAATTCACATC
2676956 C
1 C
2676957 TAGGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (11 bp):
CAATTCACATC
Found at i:2679250 original size:17 final size:18
Alignment explanation
Indices: 2679228--2679261 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2679218 TAATTGTGAA
2679228 TTAAAT-TATAATTATTT
1 TTAAATGTATAATTATTT
*
2679245 TTAAATGTATAGTTATT
1 TTAAATGTATAATTATT
2679262 ACAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTAAATGTATAATTATTT
Found at i:2679282 original size:27 final size:27
Alignment explanation
Indices: 2679232--2679288 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2679222 TGTGAATTAA
* *
2679232 ATTATAATTATTTTTAAATGTATAGTT
1 ATTACAATTATTTTTAAATGTATAATT
*
2679259 ATTACAATTTTTTTTAAAAT-TATAATT
1 ATTACAATTATTTTT-AAATGTATAATT
2679286 ATT
1 ATT
2679289 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (27 bp):
ATTACAATTATTTTTAAATGTATAATT
Found at i:2686036 original size:17 final size:18
Alignment explanation
Indices: 2686014--2686047 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2686004 AATCCATACA
2686014 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
*
2686031 AACTCATTCATTATCAT
1 AACTCAATCATTATCAT
2686048 TTCTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:2687904 original size:23 final size:21
Alignment explanation
Indices: 2687863--2687904 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2687853 TGAACCGTCG
*
2687863 CTCTCTTTCTTTTTCTTCTTT
1 CTCTCTTTCTGTTTCTTCTTT
2687884 CTCTCTTCTCTGTTTCGTTCT
1 CTCTCTT-TCTGTTTC-TTCT
2687905 GCTCTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.00, C:0.31, G:0.05, T:0.64
Consensus pattern (21 bp):
CTCTCTTTCTGTTTCTTCTTT
Found at i:2687966 original size:5 final size:5
Alignment explanation
Indices: 2687950--2687995 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
2687940 CTTTTGTTAT
2687950 ATATA TATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATATA A
1 ATATA -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA A
2687996 AAACATAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 23 0.62
6 9 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:2687976 original size:19 final size:19
Alignment explanation
Indices: 2687947--2687994 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
2687937 TTTCTTTTGT
2687947 TATATATATATATAAT-ATAA
1 TATA-ATATAT-TAATAATAA
2687967 TATAATATATTAATAATAA
1 TATAATATATTAATAATAA
2687986 TATAATATA
1 TATAATATA
2687995 AAAACATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 19 0.70
20 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATATATTAATAATAA
Found at i:2688004 original size:24 final size:24
Alignment explanation
Indices: 2687958--2688004 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2687948 ATATATATAT
* *
2687958 ATAATATAATATAATATATTAATA
1 ATAATATAATATAATAAAATAATA
2687982 ATAATATAATATAA-AAACATAAT
1 ATAATATAATATAATAAA-ATAAT
2688005 CATTACTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATA
Found at i:2707586 original size:22 final size:22
Alignment explanation
Indices: 2707558--2707662 Score: 156
Period size: 22 Copynumber: 4.8 Consensus size: 22
2707548 TGTTGATAGT
*
2707558 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
2707580 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
2707602 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
2707624 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
2707646 ACGTACTAAGCTCTCAT
1 ACGTACTAAGCTCTCAT
2707663 AATTTTTGCA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:2710841 original size:33 final size:33
Alignment explanation
Indices: 2710799--2710881 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
2710789 TGGAAAAGCT
**
2710799 AATATTTTCTTGTGTTTGGATGAATCTGTATAA
1 AATATTTTCTTGTGTTTAAATGAATCTGTATAA
* *
2710832 AATATTTTCTGGTGTTTAAATGAATCTGTGTAA
1 AATATTTTCTTGTGTTTAAATGAATCTGTATAA
* * *
2710865 AACATTTGCTTTTGTTT
1 AATATTTTCTTGTGTTT
2710882 TATAAAAGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (33 bp):
AATATTTTCTTGTGTTTAAATGAATCTGTATAA
Found at i:2711419 original size:26 final size:26
Alignment explanation
Indices: 2711390--2711469 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 26
2711380 AAAATAAAAT
*
2711390 TTAAATATTAAATATTAAATAATTTA
1 TTAAATAATAAATATTAAATAATTTA
*
2711416 TTAAAAATAATAAATTATATTAATAATTTA
1 TT--AAATAATAAA-TAT-TAAATAATTTA
* *
2711446 TTATATGACTAAATA-TAAATAATT
1 TTAAAT-AATAAATATTAAATAATT
2711470 AAATACGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 10 0.23
28 14 0.32
29 8 0.18
30 12 0.27
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
TTAAATAATAAATATTAAATAATTTA
Found at i:2711633 original size:31 final size:31
Alignment explanation
Indices: 2711598--2711660 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2711588 AGTAAAATTA
2711598 TCTATTGAGGAGCTCTTTTCCAGAAAATAAC
1 TCTATTGAGGAGCTCTTTTCCAGAAAATAAC
2711629 TCTATTGAGGAGCTCTTTTCCAGAAAATAAC
1 TCTATTGAGGAGCTCTTTTCCAGAAAATAAC
2711660 T
1 T
2711661 TACGCTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (31 bp):
TCTATTGAGGAGCTCTTTTCCAGAAAATAAC
Found at i:2718331 original size:17 final size:17
Alignment explanation
Indices: 2718308--2718342 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2718298 CTAACCCCTT
*
2718308 TTTTTTTTTTTTTGTAAA
1 TTTTTTTCTTTTT-TAAA
2718326 TTTTTTTCTTTTTTAAA
1 TTTTTTTCTTTTTTAAA
2718343 AAATTCCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTTTTTAAA
Found at i:2720684 original size:4 final size:4
Alignment explanation
Indices: 2720675--2720700 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2720665 ACAGTTTCGT
2720675 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
2720701 GTATGGTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2735150 original size:15 final size:16
Alignment explanation
Indices: 2735125--2735158 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2735115 CAGTTATTAT
2735125 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
2735141 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
2735156 TTT
1 TTT
2735159 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:2735438 original size:7 final size:7
Alignment explanation
Indices: 2735426--2735453 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2735416 ACATTTTCTT
2735426 AAAATTA
1 AAAATTA
2735433 AAAATTA
1 AAAATTA
2735440 AAAATTA
1 AAAATTA
2735447 AAAATTA
1 AAAATTA
2735454 CTCCATAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATTA
Found at i:2739492 original size:2 final size:2
Alignment explanation
Indices: 2739485--2739523 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2739475 ACATATCTTT
2739485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2739524 TCCTAATTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2745877 original size:2 final size:2
Alignment explanation
Indices: 2745872--2745912 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2745862 TTGGTGTGTT
2745872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2745913 TATGTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2746242 original size:20 final size:20
Alignment explanation
Indices: 2746205--2746243 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2746195 TTAATATTAC
*
2746205 AAAATTTATTATACTTAATA
1 AAAATTTATAATACTTAATA
2746225 AAAATTTAGTAATA-TTAAT
1 AAAATTTA-TAATACTTAAT
2746244 TGAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAATTTATAATACTTAATA
Found at i:2756509 original size:21 final size:21
Alignment explanation
Indices: 2756483--2756525 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2756473 ATTGGGTGGA
2756483 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
2756504 TCAGCTTTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
2756525 T
1 T
2756526 GGTATTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:2758233 original size:16 final size:16
Alignment explanation
Indices: 2758209--2758239 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2758199 AATTCGAGTT
*
2758209 GAATTTGAAAATATCC
1 GAATATGAAAATATCC
2758225 GAATATGAAAATATC
1 GAATATGAAAATATC
2758240 ATGTTGGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (16 bp):
GAATATGAAAATATCC
Found at i:2759226 original size:16 final size:15
Alignment explanation
Indices: 2759207--2759259 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2759197 TTTAGCTAAG
2759207 ATTTTTTAGATTCAAA
1 ATTTTTTAGATTC-AA
2759223 ATTTTTTTAG-TTCAA
1 A-TTTTTTAGATTCAA
*
2759238 ATTTTTTAAGATT-AG
1 ATTTTTT-AGATTCAA
2759253 ATTTTTT
1 ATTTTTT
2759260 TTTTCAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 6 0.18
15 13 0.39
16 6 0.18
17 8 0.24
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (15 bp):
ATTTTTTAGATTCAA
Found at i:2759227 original size:15 final size:16
Alignment explanation
Indices: 2759207--2759250 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
2759197 TTTAGCTAAG
2759207 ATTTTTTAGATTCAAA
1 ATTTTTTAGATTCAAA
2759223 ATTTTTTTAG-TTC-AA
1 A-TTTTTTAGATTCAAA
2759238 ATTTTTTAAGATT
1 ATTTTTT-AGATT
2759251 AGATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 6 0.24
17 8 0.32
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (16 bp):
ATTTTTTAGATTCAAA
Found at i:2759306 original size:16 final size:16
Alignment explanation
Indices: 2759260--2759307 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
2759250 TAGATTTTTT
*
2759260 TTTTCAAGTTTAAACC
1 TTTTCAAGTTTAAATC
* *
2759276 TTTTCAGGTTCAAATC
1 TTTTCAAGTTTAAATC
*
2759292 TTTTCATGTTTAAATC
1 TTTTCAAGTTTAAATC
2759308 AAATTAAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (16 bp):
TTTTCAAGTTTAAATC
Found at i:2762398 original size:11 final size:12
Alignment explanation
Indices: 2762372--2762396 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2762362 TATTAAAATG
2762372 AATTAAAAACCA
1 AATTAAAAACCA
2762384 AATTAAAAACCA
1 AATTAAAAACCA
2762396 A
1 A
2762397 TTTTTGTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (12 bp):
AATTAAAAACCA
Found at i:2763953 original size:13 final size:15
Alignment explanation
Indices: 2763923--2763955 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2763913 GTTGTGCTCA
2763923 TTTATGCTTATAATG
1 TTTATGCTTATAATG
2763938 TTTATGC-TAT-ATG
1 TTTATGCTTATAATG
2763951 TTTAT
1 TTTAT
2763956 TTGGTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 3 0.17
15 7 0.39
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTATGCTTATAATG
Found at i:2765654 original size:15 final size:16
Alignment explanation
Indices: 2765634--2765666 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2765624 CAGAATCATA
2765634 ATTCATCTCAAT-TTC
1 ATTCATCTCAATATTC
*
2765649 ATTCATTTCAATATTC
1 ATTCATCTCAATATTC
2765665 AT
1 AT
2765667 ACCTACCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTCATCTCAATATTC
Found at i:2766571 original size:13 final size:13
Alignment explanation
Indices: 2766555--2766597 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
2766545 ATAGAAAACC
2766555 ATAATAATAATTA
1 ATAATAATAATTA
*
2766568 ATAATTATAATT-
1 ATAATAATAATTA
2766580 ATAATAATAAATTA
1 ATAATAAT-AATTA
2766594 ATAA
1 ATAA
2766598 CAAAATCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATAATTA
Found at i:2792933 original size:97 final size:95
Alignment explanation
Indices: 2792811--2792997 Score: 302
Period size: 97 Copynumber: 1.9 Consensus size: 95
2792801 GTTACATATC
* * *
2792811 AAATCTGATTACATAGAGTCATCTCTCCTAATTTCTATTCTCGACAACAAAACTGTTGGTTGGTT
1 AAATCTGATTACAGAGAGTCATCTCTCCTAATCTCTATTCTCGACAACAAAACTGTTAGTTGGTT
2792876 TTGTGGTTTCGAGAATTTACAACTAGTAAA
66 TTGTGGTTTCGAGAATTTACAACTAGTAAA
* *
2792906 AAATCTGATTACAGAGAGAGTCGTCTCTCCTAATCTCTATTCTCGACAACAAAATTGTTAGTTGG
1 AAATCTGATTAC--AGAGAGTCATCTCTCCTAATCTCTATTCTCGACAACAAAACTGTTAGTTGG
*
2792971 TTTTGTGGTTTTGAGAATTTACAACTA
64 TTTTGTGGTTTCGAGAATTTACAACTA
2792998 TTTTACTATC
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 12 0.14
97 72 0.86
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (95 bp):
AAATCTGATTACAGAGAGTCATCTCTCCTAATCTCTATTCTCGACAACAAAACTGTTAGTTGGTT
TTGTGGTTTCGAGAATTTACAACTAGTAAA
Found at i:2799079 original size:18 final size:18
Alignment explanation
Indices: 2799041--2799085 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2799031 TTTTAAATAT
2799041 ATATATTTTAACCATTCTA
1 ATAT-TTTTAACCATTCTA
*
2799060 ATGATTTTTAACC-TTTTA
1 AT-ATTTTTAACCATTCTA
2799078 ATATTTTT
1 ATATTTTT
2799086 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 10 0.42
20 2 0.08
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTTTTAACCATTCTA
Found at i:2799086 original size:18 final size:19
Alignment explanation
Indices: 2799041--2799087 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
2799031 TTTTAAATAT
*
2799041 ATATATTTTAACCATTCTA
1 ATATTTTTTAACCATTCTA
*
2799060 ATGA-TTTTTAACC-TTTTA
1 AT-ATTTTTTAACCATTCTA
2799078 ATATTTTTTA
1 ATATTTTTTA
2799088 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 12 0.50
19 10 0.42
20 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAACCATTCTA
Found at i:2802030 original size:31 final size:31
Alignment explanation
Indices: 2801995--2802065 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
2801985 AAAAACACTT
* *
2801995 AATAG-TCTAGTCATTTAAATAAAAATTTTAG
1 AATAGTTC-AGTCACTTAAATAAAAATTTTAA
* *
2802026 AATAGTTCAGTGACTTAAATGAAAATTTTAA
1 AATAGTTCAGTCACTTAAATAAAAATTTTAA
*
2802057 AATAATTCA
1 AATAGTTCA
2802066 ATTACTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (31 bp):
AATAGTTCAGTCACTTAAATAAAAATTTTAA
Found at i:2805719 original size:22 final size:22
Alignment explanation
Indices: 2805678--2805719 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2805668 AAATTAAATT
* *
2805678 ATATATTTTTATGATATTAAAA
1 ATATAATTTTATCATATTAAAA
*
2805700 ATATAATTTTATCATTTTAA
1 ATATAATTTTATCATATTAA
2805720 TGATTTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATAATTTTATCATATTAAAA
Found at i:2805759 original size:25 final size:26
Alignment explanation
Indices: 2805706--2805770 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
2805696 AAAAATATAA
*
2805706 TTTTATCA-TTTT-AATGATTTATAT
1 TTTTATCATTTTTGAATGATTAATAT
* *
2805730 CTTTATAATTTTTGAATGATTAAT-T
1 TTTTATCATTTTTGAATGATTAATAT
2805755 TTTTATCATTTTTGAA
1 TTTTATCATTTTTGAA
2805771 GGATCAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 6 0.18
25 19 0.56
26 9 0.26
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTTATCATTTTTGAATGATTAATAT
Found at i:2805782 original size:25 final size:25
Alignment explanation
Indices: 2805731--2805782 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2805721 GATTTATATC
* * *
2805731 TTTATAATTTTTGAATGATTAATTT
1 TTTATAATTTTTGAAGGATCAAATT
*
2805756 TTTATCATTTTTGAAGGATCAAATT
1 TTTATAATTTTTGAAGGATCAAATT
2805781 TT
1 TT
2805783 AATTTTGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.56
Consensus pattern (25 bp):
TTTATAATTTTTGAAGGATCAAATT
Done.